Help me with molecule docking

More Manojkumar Avaghade's questions See All

How to purify all the nucleic acid (DNA and RNA) associated protein from bacteria?

08 September 2016 1,476 2 View

Can anyone provide me a M.tb glutamine synthetase clonned in e.coli?

I was having M.tb glutamine synthetase clone but due to some unavoidable situations I lost those clone. If anyone has a M.tb glutamine synthetase clonned in e.coli, I would be very thankful if...

06 July 2016 2,224 2 View

What is the optimum irreproducible retention time of the peak in HPLC?

I am doing reverse phase HPLC using C18. Keeping the flow rate and composition of solvent constant, I should get my target peak at 14 min, but I am getting the peak sometime at 14 minutes sometime...

05 June 2014 826 4 View

Can anyone tell me what kind of interaction there is between SDS and proteins in SDS-PAGE?

Does SDS forms any kind of bond with the protein? Please help with my query.

04 May 2014 8,175 11 View

waht should be a control for RNA isolation?

I am working on RNA isolation. As a positive control for RNA what should i use so that i can be sure that the method for isolation that i am doing is giving me correct result.

10 November 2011 2,002 2 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Girish Singh

Please use mvd regarding this concern ....it will obiously give u good results with graphical representationj

Simone Brogi

Fep

Hasni Arsad

I am suggesting to use glide of schrodinger suit.

Kannan M.

Hi ManojKumar, i can suggest u to use Auto-dock software it is free of cost, and if u have glide module in Schrodinger suit that will be on of the best docking software for docking analysis. If u know the active site of the target protein then ur docking will be simple but if u don't have the information about active site..it will separate story. The binding affinity of the compound can be determine using free energy binding and docking score this information u can get from auto dock as well as in glide software. First study the interacting mode of ur ligand with ur target protein then modify the ligand accordance to that of free energy and do docking with newly drawn compound. Before that u read about the docking and its analysis. I support the Brian D Marsden said. For exact binding affinity of ur ligand with ur targhet protein can be determined in experimentally using ITC or crystallography.

Shruti Pawar

Hi Manojkumar, what help do you exactly need? Being specific can fetch you a lot more valuble suggestions.

Manojkumar Avaghade

Thanks a lot guys for your replies. Actually i am not much aware of the bioinformatic sofwares so i will be very thankfull to you if you tell me what are the step to be performed in the respective softwares. guys i Know the target site where the drug molecule will go on bind to the protein. once i build a molecule which have more binding affinity to the protein than the traditional drug i am going for the crystallography to see the exact interaction. so guys please help me. thanking you.

HI manoj, If u use the free software (Autodock) then u can follow the link given below for installation of the software and tutorial for doing docking.

1. http://www.youtube.com/watch?v=LQHvlH0Hq0I&feature=related

2. http://www.youtube.com/watch?v=awGrWBEk8Q0&feature=related

3. http://www.youtube.com/watch?v=H_ChiGTpZd4&feature=related

4. http://www.youtube.com/watch?v=KScj5jpAlno&feature=related

5. http://www.youtube.com/watch?v=zZdr2LwPIqg&feature=related

hi manoj, if u plan to use free software u can use autodock. Installation of the software and running program u can follow the link.

http://www.youtube.com/watch?v=LQHvlH0Hq0I&feature=related

U can use tutorial for that

Ajao Abdullahi

Thanks, I am also interested in docking my protein with different isomers of a compound (ligand).How do I interprete my result so that I can mutate at particular C-position? to ensure & improve high catalytic property of my protein.

hi Ajao, If u are using isomers for docking analysis and u want to interpret the results u should have chemistry knowledge or u can get literature information. Some people already down so many docking work using isomers if u refer that it will be useful for u to interpret ur docking results.

Thanks Kannan, I 'll get back to you!

hi Ajao,

here i have attached tutorial which we used for previous workshop conducted in pondicherry university, it might help u............. this tutorial is based on autodock software.......

Vikash Kumar

hi Manoj, AUTODOCK is good for docking small molecules to the ligand/sbstrate binding site.Docking programs not always give u the correct quantitative information about binding, but it may give u a probable binding mode.

Kanan,

I am so much grateful, is very helpful.Thanks